Summary

Target folder: C:/Git/ETN_workshop_Jan2021/actel_example

Timestamp: 2021-01-25 15:31:21

Number of target tags: 60

Number of listed receivers: 17 (of which 1 had no detections)

Data time range: 2018-04-13 22:26:37 to 2018-05-25 17:46:13 (Europe/Copenhagen).

Percentage of post-release valid detections: 100%

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Study area

Arrays with the same background belong to the same section. Release sites are marked with “R.S.”. Arrays connected with an arrow indicate that the animals can only pass in one direction.

Receiver stations

Station.name Latitude Longitude x y Array Section Standard.name
Station -1 56.35474 8.629019 477075.2 6245625 A0 River St.1
Station 1 56.35672 8.603097 475474.6 6245854 A1 River St.2
Station 2 56.36505 8.510094 469734.4 6246818 A2 River St.3
Station 3 56.34976 8.385683 462033.4 6245178 A3 River St.4
Station 4 56.32894 8.309133 457279.2 6242906 A4 River St.5
Station 5 56.32576 8.306444 457109.4 6242553 A5 River St.6
Station 6 56.32267 8.303267 456909.4 6242211 A6 River St.7
Station 7 56.32865 8.249125 453568.3 6242912 A7 Fjord St.8
Station 8 56.32610 8.246447 453399.6 6242630 A7 Fjord St.9
Station 9 56.32388 8.240797 453047.5 6242387 A7 Fjord St.10
Station 10 56.32192 8.239672 452975.5 6242169 A7 Fjord St.11
Station 11 56.37173 8.132342 446407.4 6247792 A8 Fjord St.12
Station 12 56.37221 8.130017 446264.5 6247847 A8 Fjord St.13
Station 13 56.37250 8.127761 446125.6 6247881 A8 Fjord St.14
Station 14 56.37199 8.118439 445549.1 6247831 A9 Sea St.15
Station 15 56.37256 8.118169 445533.2 6247895 A9 Sea St.16
Station 16 56.37200 8.117658 445500.9 6247833 A9 Sea St.17

Deployments

Receiver Array Station.name Standard.name Start Stop
132907 A0 Station -1 St.1 2018-03-15 12:00:00 2018-06-01 12:00:00
132908 A1 Station 1 St.2 2018-03-15 12:00:00 2018-06-01 12:00:00
132909 A7 Station 7 St.8 2018-03-15 12:00:00 2018-06-01 12:00:00
132914 A5 Station 5 St.6 2018-03-15 12:00:00 2018-06-01 12:00:00
132915 A6 Station 6 St.7 2018-03-15 12:00:00 2018-06-01 12:00:00
132916 A4 Station 4 St.5 2018-03-15 12:00:00 2018-06-01 12:00:00
132917 A3 Station 3 St.4 2018-03-15 12:00:00 2018-06-01 12:00:00
132918 A2 Station 2 St.3 2018-03-15 12:00:00 2018-06-01 12:00:00
133205 A8 Station 13 St.14 2018-03-15 12:00:00 2018-06-01 12:00:00
133206 A9 Station 16 St.17 2018-03-15 12:00:00 2018-06-01 12:00:00
133209 A8 Station 12 St.13 2018-03-15 12:00:00 2018-06-01 12:00:00
133210 A9 Station 14 St.15 2018-03-15 12:00:00 2018-06-01 12:00:00
133215 A9 Station 15 St.16 2018-03-15 12:00:00 2018-06-01 12:00:00
133220 A8 Station 11 St.12 2018-03-15 12:00:00 2018-06-01 12:00:00
133221 A7 Station 10 St.11 2018-03-15 12:00:00 2018-06-01 12:00:00
133222 A7 Station 8 St.9 2018-03-15 12:00:00 2018-06-01 12:00:00
133224 A7 Station 9 St.10 2018-03-15 12:00:00 2018-06-01 12:00:00

Release sites

Station.name Latitude Longitude x y Array Type Standard.name n.A n.B
RS1 56.349 8.6204 476539 6244988 A1 Release RS1 30 30

Array forward efficiency

Note:
These efficiency calculations do not account for backwards movements. This implies that the total number of animals to have been last seen at a given array may be lower than the displayed below. Please refer to the section survival overview and last seen arrays to find out how many animals were considered to have disappeared per section.
The data used in the tables below is stored in the overall.CJS object. Auxiliary information can also be found in the matrices and arrays objects.
These efficiency values are estimated using the analytical equations provided in the paper “Using mark-recapture models to estimate survival from telemetry data” by Perry et al. (2012). In some situations, more advanced efficiency estimation methods may be required.
You can try running advEfficiency(results$overall.CJS) to obtain beta-drawn efficiency distributions (replace results with the name of the object where you saved the analysis).

Individuals detected and estimated

A0 A1 A2 A3 A4 A5 A6 A7 A8 A9
detected 0 54 54 52 52 52 52 49 44 35
here plus on peers - 54 54 50 52 52 50 43 35 -
not here but on peers - 0 0 2 0 0 0 1 0 -
known 0 54 54 54 52 52 52 50 44 35
estimated - 54 54 54 52 52 52 50 44 -

Array efficiency

Note: These values already include any intra-array efficiency estimates that have been requested.

A0 A1 A2 A3 A4 A5 A6 A7 A8 A9
efficiency - 100% 100% 96.2% 100% 100% 100% 97.7% 100% -

Warning messages

Warning: GUI is set to 'needed' but packages 'gWidgets2', 'gWidgets2RGtk2', 'RGtk2' are not available. Please install them if you intend to run GUI.
         Disabling GUI (i.e. GUI = 'never') for the current run.
Warning: No detections were found for receiver(s) 132907.
Warning: 'success.arrays' was not defined. Assuming success if the tags are last detected at array A9.
Warning: 'speed.warning'/'speed.error' were not set, skipping speed checks.
Warning: 'inactive.warning'/'inactive.error' were not set, skipping inactivity checks.
Warning: Inter-section backwards movements were detected for tag R64K-4508 (30/54).
Warning: Inter-section backwards movements were detected for tag R64K-4526 (45/54).
Warning: No tags passed through array A0. Skipping efficiency estimations for this array.

User comments

No comments were included during the analysis.

Biometric graphics

Note:
The data used in this graphic is the data present in the biometrics.csv file.

Section Survival

Note:
The data used in this table and graphic is stored in the section.overview object.
Total Disap..in.River Migrated.to.Fjord Disap..in.Fjord Migrated.to.Sea Disap..in.Sea Succeeded
A 30 4 26 1 25 5 20
B 30 4 26 7 19 4 15

Last Seen Arrays

Note:
The data used in this graphic is stored in the status.df object (‘Very.last.array’ column).

Progression

Zoom in or open the figure in a new tab to clearly read the text within each circle.

Note:
The progression calculations do not account for backwards movements. This implies that the total number of animals to have been last seen at a given array may be lower than the displayed below. Please refer to the section survival overview and last seen arrays to find out how many animals were considered to have disappeared per section.
The data used in this graphic is stored in the overall.CJS object, and the data used in the tables is stored in the group.overview object. You can find detailed progressions per release site in the release.overview object.

Group: A

Release A0 A1 A2 A3 A4 A5 A6 A7 A8 A9
detected 30 0 26 26 25 26 26 26 26 25 20
here plus on peers - - 26 26 25 26 26 26 25 20 -
not here but on peers - - 0 0 1 0 0 0 0 0 -
known 30 0 26 26 26 26 26 26 26 25 20
estimated - - 26 26 26 26 26 26 26 25 -
difference - - 0 0 0 0 0 0 0 0 -

Group: B

Release A0 A1 A2 A3 A4 A5 A6 A7 A8 A9
detected 30 0 28 28 27 26 26 26 23 19 15
here plus on peers - - 28 28 25 26 26 24 18 15 -
not here but on peers - - 0 0 1 0 0 0 1 0 -
known 30 0 28 28 28 26 26 26 24 19 15
estimated - - 28 28 28 26 26 26 24 19 -
difference - - 0 0 0 0 0 0 0 0 -

Time of arrival at each Array

Note:
Coloured lines on the outer circle indicate the mean value for each group and the respective ranges show the standard error of the mean. Each group’s bars sum to 100%. The number of data points in each group is presented between brackets in the legend of each pannel.
You can replicate these graphics and edit them as needed using the plotTimes() function.
The data used in these graphics is stored in the times object.
C:/actel_report_auxiliary_files/circular_svg_print_failure_bounce_back.png C:/actel_report_auxiliary_files/circular_svg_print_failure_bounce_back.png C:/actel_report_auxiliary_files/circular_svg_print_failure_bounce_back.png C:/actel_report_auxiliary_files/circular_svg_print_failure_bounce_back.png C:/actel_report_auxiliary_files/circular_svg_print_failure_bounce_back.png

Dotplots

Note:
The top 10% of the values for each panel are marked in red.
The bottom 10% of the values for each panel are marked in blue.
The columns starting with “To” should be read as either “Average time to …” or “Average speed to …”, depending on the unit used. The columns starting with “In” should be read as “Total time in …”. These reductions were made to keep the column headers as short as possible.
The data used in these graphics is stored in the status.df object.

Individual detection plots

Note:
You can choose to plot detections by station or by array using the detections.y.axis argument.
The detections are coloured by section. The vertical black dashed line shows the time of release. The vertical grey dashed lines show the assigned moments of entry and exit for each study area section. The full dark-grey line shows the movement events considered valid, while the dashed dark-grey line shows the movement events considered invalid.
Manually edited tag detections are highlighted with yellow graphic borders.
Manually overridden tag detections are highlighted with red graphic borders.
The arrays have been aligned by section, following the order provided either in the spatial input or the section.order argument.
You can replicate these graphics and edit them as needed using the plotDetections() function.
You can also see the movement events of multiple tags simultaneously using the plotMoves() function.
The data used in these graphics is stored in the detections and movements objects (and respective valid counterparts).

Sensor plots

Note:
The colouring in these plots will follow that of the individual detection plots, which can be modified using detections.y.axis.
The data used for these graphics is stored in the valid.detections object.
You can replicate these graphics and edit them as needed using the plotSensors() function.

Full log

Actel R package report.
Version: 1.2.1

Target folder: C:/Git/ETN_workshop_Jan2021/actel_example
Timestamp: 2021-01-25 15:31:21
Function: migration()

M: 'report' option has been activated.
M: Importing data. This process may take a while.
M: Number of target tags: 60.
M: Matching detections with deployment periods.
M: Number of ALS: 17 (of which 1 had no detections)
Warning: No detections were found for receiver(s) 132907.
M: Data time range: 2018-04-13 22:26:37 to 2018-05-25 17:46:13 (Europe/Copenhagen).
M: File 'distances.csv' found, activating speed calculations.
M: Data successfully imported!
Warning: 'success.arrays' was not defined. Assuming success if the tags are last detected at array A9.
M: Creating movement records for the valid tags.
M: Checking movement events quality.
Warning: 'speed.warning'/'speed.error' were not set, skipping speed checks.
Warning: 'inactive.warning'/'inactive.error' were not set, skipping inactivity checks.
M: Compiling and checking section movements for the valid tags.
Warning: Inter-section backwards movements were detected for tag R64K-4508 (30/54).
Warning: Inter-section backwards movements were detected for tag R64K-4526 (45/54).
M: Filtering valid array movements.
M: Filtering valid section movements.
M: Compiling migration timetable.
M: Compiling summary information tables.
Warning: No tags passed through array A0. Skipping efficiency estimations for this array.
M: Calculating array efficiency.
M: Saving results as 'actel_migration_results.RData'.
M: Producing the report.
M: Drawing individual detection graphics.
M: Printing sensor values for tags with sensor data.
M: Process finished successfully.

-------------------
User interventions:
-------------------
n # invalidate/expand moves in R64K-4508?
n # invalidate/expand moves in R64K-4526?
y # save results?
-------------------
Function call:
-------------------
migration(tz = 'Europe/Copenhagen', section.order = NULL, datapack = NULL, success.arrays = NULL, max.interval = 60, minimum.detections = 2, start.time = NULL, stop.time = NULL, speed.method = 'last to first', speed.warning = NULL, speed.error = NULL, jump.warning = 2, jump.error = 3, inactive.warning = NULL, inactive.error = NULL, exclude.tags = NULL, override = NULL, report = TRUE, auto.open = TRUE, discard.orphans = FALSE, discard.first = NULL, save.detections = FALSE, if.last.skip.section = TRUE, replicates = NULL, disregard.parallels = TRUE, GUI = 'never', save.tables.locally = FALSE, print.releases = TRUE, detections.y.axis = 'auto')
-------------------

Index:

Summary Study area Stations Deployments Release sites Array efficiency Warnings Comments Biometrics Section survival Last seen Progression Arrival times Dotplots Individual detections Sensor data Full log